Professor

School of Basic Medical Sciences

Southern Medical University

present - 2018

• 2021-present, Director, Department of Bioinformatics
• 2019-2021, Associate director, Department of Bioinformatics

Post-doctoral Fellow

State Key Laboratory of Infectious Diseases

The University of Hong Kong

2018 - 2017

Bioinformatician

Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes

Jinan University

2013 - 2009

PhD., Bioinformaitcs

The University of Hong Kong

Hong Kong, CN

2017 - 2013

• Thesis: Big-data computational methods for studying molecular evolution: from accurate genome assembly to phylogenetic analysis and data integration

M.S., Biochemistry and Molecular Biology

Anhui Medical University

Hefei, CN

2009 - 2006

• Thesis: miRNA靶基因计算分析新方法及其应用研究

B.S., Biotechnology

South China Agricultural University

Guangzhou, CN

2005 - 2001

Antigenic cartography and antibody landscapes course

University of Cambridge

Cambridge, UK

2019

南方医科大学高层次人才“不忘初心 牢记使命”学习教育

延安干部培训学院

Yan’an, CN

2018

Train the Trainers

Institut Pasteur

Paris, FR

2015

Visiting student

Beijing Institute of Radiation Medicine

Beijing, CN

2009 - 2007

高等学校教师资格

广东省教育厅

N/A

2019

Certificate of Teaching and Learning in Higher Education

Centre for Enhancement of Teaching and Learning

The University of Hong Kong

2015

2020全球前2%顶尖科学家

美国斯坦福大学

N/A

2021

2020年中国高被引学者

Elsevier

N/A

Postgraduate studentships

The University of Hong Kong

N/A

2017 - 2013

Best paper of the year 2010

Journal of Integrated OMICS

N/A

2012

大样本多组学数据联合分析系统研究与构建 (K921280198)

主持, CNY ¥600,000, 中央军委科学技术委员会, 国防科技创新特区163计划

N/A

2022 - 2020

南方医科大学第三层次人才引进科研项目 (G618289088)

主持, CNY ¥1,500,000

N/A

2020 - 2018

病毒性新发传染病的研究与防治 (2017YFE0190800)

参与, CNY ¥990,000, 中华人民共和国科学技术部，国家重点研发计划

N/A

hnRNPK蛋白在调控人肺癌细胞周期胞质分裂中的作用研究 (21613414)

主持, CNY ¥100,000, 中央高校基本科研业务费专项资金

N/A

2013

Hela细胞周期动态蛋白质组学分析 (21611303)

主持, CNY ¥20,000, 中央高校基本科研业务费专项资金

N/A

2011

Gene Ontology Semantic Similarity Analysis Using GOSemSim

Methods in Molecular Biology, 2117:207-215.

N/A

2020

• G Yu
• In: Kidder B. (eds) Stem Cell Transcriptional Networks
• Humana, New York, NY

生物信息学II

《功能蛋白质研究》. 385-425.

N/A

2012

• 余光创
• 何庆瑜（主编），科学出版社
• “十二五”国家重点图书出版规划项目

基础医学研究与医学发展

School of Basic Medical Sciences

Southern Medical University

2021

• Undergraduate level class

生物信息学科研训练

School of Basic Medical Sciences

Southern Medical University

2021 - 2019

• Undergraduate level class

基因组学

School of Basic Medical Sciences

Southern Medical University

• Undergraduate level class

基础医学新进展讲座

School of Basic Medical Sciences

Southern Medical University

• Undergraduate level class

BMB209: Workshops in Applied Bioinformatics

Department of Biochemistry and Molecular Biology

University of Southern Denmark

2019

• PhD level class, invited lecture

功能蛋白质研究

College of Life Science and Technology

Jinan University

2012 - 2011

• Graduate level class

Use ggbreak to effectively utilize plotting space to deal with large datasets and outliers

Frontiers in Genetics. 2021, 12:774846.

N/A

2021

• S Xu^#, M Chen^#, T Feng, L Zhan, L Zhou, G Yu^*

ggVennDiagram: An intuitive, easy-to-use, and highly customizable R package to generate Venn diagram

Frontiers in Genetics. 2021, 12:706907.

N/A

• CH Gao, G Yu, P Cai^*

ggtreeExtra: Compact visualization of richly annotated phylogenetic data

Molecular Biology and Evolution. 2021, 38(9):4039-4042.

N/A

• S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L Zhan, T Wu, E Hu, Y Jiang^*, X Bo^*, G Yu^*

clusterProfiler 4.0: A universal enrichment tool for interpreting omics data

The Innovation. 2021, 2(3):100141.

N/A

• T Wu^#, E Hu^#, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo^*, G Yu^*

IOBR: Multi-Omics Immuno-Oncology Biological Research to Decode Tumor Microenvironment and Signatures

Frontiers in Immunology. 2021, 12:687975.

N/A

• D Zeng^#, Z Ye^#, R Shen, G Yu, J Wu, Y Xiong, R Zhou, W Qiu, N Huang, L Sun, X Li, J Bin, Y Liao, M Shi, W Liao^*

nCov2019: an R package for studying the COVID-19 coronavirus pandemic

PeerJ. 2021, 9:e11421.

N/A

• T Wu, E Hu, X Ge^*, G Yu**^*

TreeSummarizedExperiment: a S4 class for data with hierarchical structure

F1000Research. 2021, 9:1246.

N/A

• R Huang, C Soneson, FGM Ernst, KC Rue-Albrecht, G Yu, SC Hicks, MD Robinson^*

Identification of prognostic Stromal-Immune Score-Based Genes in Hepatocellular Carcinoma microenvironment

Frontiers in Genetics. 2021, 12: 625236.

N/A

• S Liu, G Yu^*, L Liu^*, X Zou, L Zhou, E Hu, Y Song

Gut microbiota and metabolite alterations associated with reduced bone mineral density or bone metabolic indexes in postmenopausal osteoporosis

Aging (Albany NY). 2020, 12(9):8583-8604.

N/A

2020

• J He^#, S Xu^#, B Zhang, C Xiao, Z Chen, F Si, J Fu, X Lin, G Zheng^*, G Yu^*, J Chen^*

Using ggtree to Visualize Data on Tree-Like Structure

Current Protocols in Bioinformatics, 69(1):e96

N/A

• G Yu^*

treeio: an R package for phylogenetic tree input and output with richly annotated and associated data

Molecular Biology and Evolution. 2020, 37(2):599-603.

N/A

• LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu^*
• Impact Factor = 14.797

RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms

PeerJ Computer Science. 2020, 6:e251.

N/A

• Z Hao, D Lv, Y Ge, J Shi, D Weijers, G Yu^*, J Chen^*

Two methods for mapping and visualizing associated data on phylogeny using ggtree

Molecular Biology and Evolution. 2018, 35(12):3041-3043.

N/A

2018

• G Yu^*, TTY Lam, H Zhu, Y Guan^*
• Impact Factor = 14.797

Using meshes for MeSH term enrichment and semantic analyses

Bioinformatics. 2018, 34(21):3766–3767.

N/A

• G Yu^*

ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

Methods in Ecology and Evolution. 2017, 8(1):28-36

N/A

2017

• G Yu, DK Smith, H Zhu, Y Guan, TTY Lam^*
• ESI Highly Cited Paper

ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization

Molecular BioSystems. 2016, 12(2):477-479

N/A

2016

• G Yu, QY He^*
• ESI Highly Cited Paper

Integrated Translatomics with Proteomics to Identify Novel Iron–Transporting Proteins in Streptococcus pneumoniae

Frontiers in Microbiology. 2016, 7:78

N/A

• XY Yang, K He, G Du, X Wu, G Yu, Y Pan, G Zhang^*, X Sun^*, QY He^*

Genetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015

Infection, Genetics and Evolution. 2016, 38:96-100

N/A

• PY Huang, CCD Lee, CH Yip, CL Cheung, G Yu, TTY Lam, DK Smith, H Zhu^*, Y Guan^*

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparision and visualization

Bioinformatics. 2015, 31(14):2382-2383

N/A

2015

• G Yu^*, LG Wang, QY He^*
• ESI Highly Cited Paper

DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis

Bioinformatics. 2015, 31(4):608-609

N/A

• G Yu^*, LG Wang, GR Yan, QY He^*
• ESI Highly Cited Paper

ACK1 Promotes Gastric Cancer Epithelial-Mesenchymal Transition and Metastasis through AKT-POU2F1-ECD Signaling

Journal of Pathology. 2015, 236(2):175-185

N/A

• SH Xu, JZ Huang, ML Xu, G Yu, XF Yin, D Chen^*, GR Yan^*

Proteomic analysis on the copper resistance of Streptococcus pneumonia

Metallomics. 2015, 7(3):448-454

N/A

• Z Guo, J Han, XY Yang, K Cao, K He, G Du, G Zeng, L Zhang, G Yu, Z Sun, QY He^*, X Sun^*

Proteomic analysis on the antibacterial activity of a Ru(II) complex against Strepococcus pneumonia

Journal of Proteomics. 2015, 115:107-116

N/A

• XY Yang, L Zhang, J Liu, N Li, G Yu, K Cao, J Han, G Zeng, Y Pan, X Sun^*, QY He^*

Proteomic analysis of putative heme-binding proteins in Streptococcus pyogenes

Metallomics. 2014, 6(8):1451-1459

N/A

2014

• N Wang^#, J Zhang^#, L Zhang, XY Yang, N Li, G Yu, J Han, K Cao, Z Guo, X Sun^*, QY He^*

Putative cobalt- and nickel-binding proteins and motifs in Streptococcus pneumonia

Metallomics. 2013, 5(7):928-935

N/A

2013

• X Sun^#, G Yu^#, Q Xu, N Li, C Xiao, X Yin, K Cao, J Han, QY He^*

A novel andrographolide derivative AL-1 exerts its cytotoxicity on K562 cells through a ROS-dependent mechanism

Proteomics, 2013, 13(1):169-178

N/A

• YY Zhu^#, G Yu^#, Y Zhang, Z Xu, YQ Huang, GR Yan^*, QY He^*

A DNA-Based Semantic Fusion Model for Remote Sensing Data

PLoS One. 2013, 8(10):e77090

N/A

• H Sun^*, J Weng, G Yu, RH Massawe

Quantitative Proteomics Characterization on the Anti-tumor Effects of Isodexyelephantopin against Nasopharyngeal Carcinoma

Proteomics. 2013, 13(21):3222-3232

N/A

• GR Yan^#, Z Tan^#, Y Wang, ML Xu, G Yu, Y Li^*, QY He^*

Design, SAR, angiogenic activities evaluation and pro-angiogenic mechanism of new marine cyclopeptide analogs

Current Medicinal Chemistry. 2013, 20(9):1183-1194

N/A

• J Li, X Lu, Q Wu, G Yu, Z Xu, L Qiu, Z Pei, Y Lin, J Pang^*

Proteomic investigation of the interactome of FMNL1 in hematopoietic cells unveils a role in calcium-dependent membrane plasticity

Journal of Proteomics. 2013, 78:72-82

N/A

• Y Han, G Yu, H Sarioglu, A Caballero-Martinez, F Schlott, M Ueffing, H Haase, C Peschel, AM Krackhardt^*

LXtoo: an integrated live Linux distribution for the bioinformatics community

BMC Research Notes. 2012, 5(1):360

N/A

2012

• G Yu^#, LG Wang^#, XH Meng, QY He^*

clusterProfiler: an R package for comparing biological themes among gene clusters

OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287

N/A

• G Yu, LG Wang, Y Han, QY He^*
• ESI Highly Cited Paper

Cellular MicroRNA let-7c Inhibits M1 Protein Expression of the H1N1 Influenza A Virus in Infected Human Lung Epithelial Cells

Journal of Cellular and Molecular Medicine. 2012, 16(10):2539-2546

N/A

• Y Ma^#, J Yang^#, X Fan^#, H Zhao, W Hu, Z Li, G Yu, X Ding, J Wang, X Bo, X Zheng, Z Zhou^*, S Wang^*

Genistein-induced mitotic arrest of gastric cancer cells by downregulating KIF20A, a proteomics study

Proteomics. 2012, 12(14):2391-2399

N/A

• GR Yan^#, FY Zhou^#, BL Dang, Y Zhang, G Yu, X Liu, QY He^*

Functional similarity analysis of human virus-encoded miRNAs

Journal of Clinical Bioinformatics. 2011, 1(1):15

N/A

2011

• G Yu, QY He^*

A new method for measuring functional similarity of microRNAs

Journal of Integrated OMICS. 2011, 1(1):49-54

N/A

• G Yu^#, CL Xiao^#, X Bo, CH Lu, Y Qin, S Zhan, QY He^*

Phosphoproteome profile of human lung cancer cell line A549

Molecular BioSystems. 2011, 7(2):472-479

N/A

• G Yu^#, CL Xiao^#, CH Lu^#, HT Jia, F Ge, W Wang, XF Yin, HL Jia, JX He^*, QY He^*

Proteomic Analysis of Membrane Proteins from Streptococcus pneumoniae with Multiple Separation Methods plus High Accuracy Mass Spectrometry

OMICS: A Journal of Integrative Biology. 2011, 15(10):683-694

N/A

• X Sun^#, XY Yang^#, XF Yin, G Yu, CL Xiao, X He, QY He^*

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

Bioinformatics. 2010, 26(7):976-978

N/A

2010

• G Yu^#, F Li^#, Y Qin, X Bo^*, Y Wu, S Wang^*
• ESI Highly Cited Paper

结合基因组分析预测炎症相关miRNA及其靶标

军事医学科学院院刊. 2009, 33(3):245-247

N/A

2009

• 余光创，王超，许尹，伯晓晨，王升启^*，秦宜德^*

依赖于5’端非编码区高级结构的真核生物mRNA翻译调控

中国生物化学与分子生物学报. 2007, 23(11):881-887

N/A

2007

• 余光创，秦宜德，伯晓晨，王升启^*

clusterProfiler 4.0: A universal enrichment tool for interpreting omics data

The 7^th National Conference on Computational Biology and Bioinformatics

N/A

2021

Data integration and visualization of phylogenetic trees

BioC Asia, Oct 2020

Virtual Conference

2020

R语言在生物信息学数据可视化中的应用

第八届南方医院博士论坛 - 研而有信之修“生”养“信”, Oct 2019

Southern Medical University

2019

Data integration and visualization of phylogenetic trees

Managing Zoonotic Infections in the era of One Health, Oct 2019

Guangzhou Medical University

R包开发十条建议

第一届生信人才发展论坛

Zhuhai, CN

Two methods for mapping and visualizing associated data on phylogeny using ggtree

第一届南方医科大学基础医学学术年会, Jan 2019

Southern Medical University

ggtree for tree visualization & annotation

Phylogenetic tree visualization workshop/hackathon, May 2017

The Field Museum of Natural History

2017

Computational Methods in Ecology and Evolution

The Second International Workshop on Environmental Microbiomes, Apr 2017

Sun Yat-sen University

R语言与生物信息学

潮博沙龙

Guangzhou, CN

2016

ggtree for visualization and annotation of phylogenetic trees

The 9^th China-R Conference, May 2016

Renmin University of China

中国生物工程学会

计算生物学与生物信息学专业委员会委员

N/A

present - 2021

广东省精准医学应用学会

微生态医学分会常务委员

Guangdong, CN

present - 2020

广东省医学会医学

遗传学分会青年委员会副主任委员

Guangdong, CN

中国计算机学会

会员

N/A

present - 2019

香港大学校友会

会员

N/A

present - 2017

广东潮博智库

专家

Guangdong, CN

present - 2014

International Society for Influenza and other Respiratory Virus Disease

Member

N/A

2016

International Network for Data Analysis

Steering Committee

Institut Pasteur

2015